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Hydrogen bonds

Genetics as it applies to evolution, molecular biology, and medical aspects.

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Hydrogen bonds

Postby rooboy100 » Mon Jul 18, 2005 11:49 am

I'm just wondering which enzyme is used to rejoin hydrogen bonds between complementary DNA nucleotides.

Thanks
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Postby victor » Mon Jul 18, 2005 12:02 pm

I think it's because of renaturation by giving it a cold temperature and acid to lower the pH.
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Postby rooboy100 » Mon Jul 18, 2005 12:34 pm

hmm i'm sort of looking for a specific enzyme...
but thinks anyway! :D
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Postby mith » Mon Jul 18, 2005 1:51 pm

DNA polymerase attaches the bases but I think the hydrogen bonds don't need extra help attaching to each other.
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Postby chemistry_freako » Mon Jul 18, 2005 3:21 pm

Hmms yea agreed.. DNa ligases should be up to the task - but it all depends on whether the cut strands are blunt ends or sticky ends :D
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Postby MrMistery » Mon Jul 18, 2005 7:01 pm

Since the hydrogen bonds can form experimentaly be increasing temperature slowly it is abvoius that no enzyme is needed
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i can help u

Postby ginny » Tue Jul 19, 2005 12:08 am

:) which enzyme is used to rejoin hydrogen bonds between complementary DNA nucleotides???

In general, DNA is replicated by uncoiling of the helix, strand separation by breaking of the hydrogen bonds between the complementary strands, and synthesis of two new strands by complementary base pairing. Replication begins at a specific site in the DNA called the origin of replication.

DNA replication is bidirectional from the origin of replication.To begin DNA replication, unwinding enzymes called DNA helicases cause the two parent DNA strands to unwind and separate from one another at the origin of replication to form two "Y"-shaped replication fork .These replication forks are the actual site of DNA copying. Helix destabilizing proteins bind to the single-stranded regions so the two strands do not rejoin. Enzymes called topoisimerases produce breaks in the DNA and then rejoin them in order to relieve the stress in the helical molecule during replication.

As the strands continue to unwind and separate in both directions around the entire DNA molecule, new complementary strands are produced by the hydrogen bonding of free DNA nucleotides with those on each parent strand. As the new nucleotides line up opposite each parent strand by hydrogen bonding, enzymes called DNA polymerases join the nucleotides by way of phosphodiester bonds. Actually, the nucleotides lining up by complementary base pairing are deoxynucleoside triphosphates, composed of a nitrogenous base, deoxyribose, and three phosphates. As the phosphodiester bond forms between the 5' phosphate group of the new nucleotide and the 3' OH of the last nucleotide in the DNA strand, two of the phosphates are removed providing energy for bonding. In the end, each parent strand serves as a template to synthesize a complementary copy of itself, resulting in the formation of two identical DNA molecules. During this process, the DNA molecules may attach to the cytoplasmic membrane and, as the cell elongates, the two DNA molecules are physically separated.
In reality, DNA replication is more complicated than this because of the nature of the DNA polmerases. DNA polymerase enzymes are only able to join the phosphate group at the 5' carbon of a new nucleotide to the hydroxyl (OH) group of the 3' carbon of a nucleotide already in the chain. As a result, DNA can only be synthesized in a 5' to 3' direction while copying a parent strand running in a 3' to 5' direction. Remember as mentioned above, each DNA strand has two ends. The 5' end of the DNA is the one with the terminal phosphate group on the 5' carbon of the deoxyribose; the 3' end is the one with a terminal hydroxyl (OH) group on the deoxyribose of the 3' carbon of the deoxyribose. The two strands are antiparallel, that is they run in opposite directions. Therefore, one parent strand - the one running 3' to 5' and called the leading strand - can be copied directly down its entire length. However, the other parent strand - the one running 5' to 3' and called the lagging strand - must be copied discontinuously in short fragments (Okazaki fragments) of around 100-1000 nucleotides each as the DNA unwinds.

In addition, DNA polymerase enzymes cannot begin a new DNA chain from scratch. They can only attach new nucleotides onto 3' OH group of a nucleotide in a preexisting strand. Therefore, to start the synthesis of the leading strand and each DNA fragment of the lagging strand, an RNA polymerase complex called a primosome or primase is required. The primase, which is capable of joining RNA nucleotides without requiring a preexisting strand of nucleic acid, first adds several comlementary RNA nucleotides opposite the DNA nucleotides on the parent strand. This forms what is called an RNA prime.

DNA polymerase III then replaces the primase and is able to add DNA nucleotides to the RNA primer. Later, DNA polymerase II digests away the RNA primer and replaces the RNA nucleotides of the primer with the proper DNA nucleotides to fill the g. Finally, the DNA fragments themselves are hooked together by the enzyme DNA ligase. Yet even with this complicated procedure, a 1000 micrometer-long macromolecule of tightly-packed, supercoiled DNA can make an exact copy of itself in only about 10 minutes time under optimum conditions, inserting nucleotides at a rate of about 1000 nucleotides per second!

In reality, DNA replication is more complicated than this because of the nature of the DNA polmerases. DNA polymerase enzymes are only able to join the phosphate group at the 5' carbon of a new nucleotide to the hydroxyl (OH) group of the 3' carbon of a nucleotide already in the chain. As a result, DNA can only be synthesized in a 5' to 3' direction while copying a parent strand running in a 3' to 5' direction. Remember as mentioned above, each DNA strand has two ends. The 5' end of the DNA is the one with the terminal phosphate group on the 5' carbon of the deoxyribose; the 3' end is the one with a terminal hydroxyl (OH) group on the deoxyribose of the 3' carbon of the deoxyribose. The two strands are antiparallel, that is they run in opposite directions. Therefore, one parent strand - the one running 3' to 5' and called the leading strand - can be copied directly down its entire length. However, the other parent strand - the one running 5' to 3' and called the lagging strand (def) - must be copied discontinuously in short fragments (Okazaki fragments) of around 100-1000 nucleotides each as the DNA unwinds.

In addition, DNA polymerase enzymes cannot begin a new DNA chain from scratch. They can only attach new nucleotides onto 3' OH group of a nucleotide in a preexisting strand. Therefore, to start the synthesis of the leading strand and each DNA fragment of the lagging strand, an RNA polymerase complex called a primosome or primase is required. The primase, which is capable of joining RNA nucleotides without requiring a preexisting strand of nucleic acid, first adds several comlementary RNA nucleotides opposite the DNA nucleotides on the parent strand. This forms what is called an RNA primer.

DNA polymerase III then replaces the primase and is able to add DNA nucleotides to the RNA primer. Later, DNA polymerase II digests away the RNA primer and replaces the RNA nucleotides of the primer with the proper DNA nucleotides to fill the gap. Finally, the DNA fragments themselves are hooked together by the enzyme DNA ligase. Yet even with this complicated procedure, a 1000 micrometer-long macromolecule of tightly-packed, supercoiled DNA can make an exact copy of itself in only about 10 minutes time under optimum conditions, inserting nucleotides at a rate of about 1000 nucleotides per second!


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Postby rooboy100 » Tue Jul 19, 2005 2:20 am

Wow, thank you everyone... especialy you ginny, it helped alot :)
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